avica 0.3.1.0__tar.gz

avica-0.3.1.0/.github/workflows/build_wheels.yml

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+name: Build Wheels
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        # with:
+        #   submodules: recursive     # for jive scripts
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.4.1
+        env:
+          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        # with:
+        #     submodules: recursive   # for jive scripts
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    name: Upload to PyPI
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          merge-multiple: true
+          path: dist
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

avica-0.3.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*.ms/
+*.ms
+table.f*_TSM1
+casa*log_*
+diag*/
+wheelhouse/*
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+src/avica/fits/
+src/avica/fitsio/
+src/avica/idifits/
+docs/source/_static/avica_demo.gif
+docs/source/_static/vasco_demo.gif
+src/avica/fitsioutil/__init__.py

avica-0.3.1.0/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "src/avica/external"]
+	path = src/avica/external
+	url = https://github.com/jive-vlbi/casa-vlbi.git

avica-0.3.1.0/.readthedocs.yaml

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+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.10"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# Optionally, but recommended,
+# declare the Python requirements required to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt
+        

avica-0.3.1.0/CHANGELOG

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+# Changelog
+
+## [0.3.1] - 2026-05-01
+
+### Added
+- Project renamed from **vasco** to **avica**.
+- Added `DeprecationWarning` for users still using the `vasco` package name.
+- Configuration support for `phref` (phase reference) observations.
+- `success_count` tracking for `avicametams`.
+- Vendored `casavlbitools` as plain files for better portability.
+
+### Changed
+- `avica.ms.polars` merged into `avica.ms.table`.
+- Optimized `preprocess_fitsidi` for faster `FREQUENCY` table reading.
+- Improved RFC value parsing using `pd.to_numeric` for better reliability.
+
+### Fixed
+- Fixed ANTAB generation imports and header parsing errors.
+- Handled empty/missing values in RFC catalog searches more gracefully.
+
+### Removed
+- Removed `avica.ms.polars` as a standalone module (merged).
+
+[unreleased]: https://github.com/avikhagol/avica/compare/v0.3.1...HEAD
+[0.3.1]: https://github.com/avikhagol/avica/compare/v0.2.0...v0.3.1
+[0.1.2] : https://github.com/avikhagol/avica/compare/v0.1.2...v0.1.5

avica-0.3.1.0/CMakeLists.txt

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+cmake_minimum_required(VERSION 3.18...3.30)
+option(BUILD_SHARED_LIBS "Build shared libraries" OFF)
+set(BUILD_SHARED_LIBS OFF CACHE BOOL "" FORCE)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON CACHE BOOL "" FORCE)
+
+project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX VERSION ${SKBUILD_PROJECT_VERSION})
+
+set_property(GLOBAL PROPERTY JOB_POOLS one_jobs=4 two_jobs=8)
+
+include(FetchContent)
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_C_STANDARD 17)
+set(CFITSIO_VERSION 4.5.0)
+
+if(DEFINED ENV{VIRTUAL_ENV})
+  set(Python3_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python3")
+endif()
+find_package(Python3 REQUIRED COMPONENTS Interpreter Development.Module)
+find_package(ZLIB REQUIRED)
+
+set(PYBIND11_NEWPYTHON ON)
+find_package(pybind11 CONFIG REQUIRED)
+
+set(USE_CURL     OFF CACHE BOOL "" FORCE)
+set(USE_PTHREADS OFF CACHE BOOL "" FORCE)
+set(SKIP_INSTALL_ALL ON CACHE BOOL "" FORCE)
+set(BUILD_TESTING OFF CACHE BOOL "" FORCE)
+set(CFITSIO_SKIP_PROGRAMS ON CACHE BOOL "" FORCE)
+
+FetchContent_Declare(cfitsio
+    URL https://github.com/HEASARC/cfitsio/archive/refs/tags/cfitsio-${CFITSIO_VERSION}.tar.gz
+)
+FetchContent_MakeAvailable(cfitsio)
+
+if(NOT TARGET cfitsio)
+  message(FATAL_ERROR "cfitsio target not found after FetchContent")
+endif()
+
+get_target_property(_type cfitsio TYPE)
+message(STATUS "cfitsio TYPE: ${_type}")
+set_target_properties(cfitsio PROPERTIES
+    POSITION_INDEPENDENT_CODE ON
+    JOB_POOL_COMPILE one_jobs
+    JOB_POOL_LINK one_jobs
+)
+
+set(FITSIDIUTIL_MODULE _core)
+pybind11_add_module(${FITSIDIUTIL_MODULE} MODULE src/avica/fitsidiutil/bindings.cpp)
+set_target_properties(${FITSIDIUTIL_MODULE} PROPERTIES
+    OUTPUT_NAME _core
+    JOB_POOL_COMPILE one_jobs
+    JOB_POOL_LINK two_jobs
+)
+
+target_link_libraries(${FITSIDIUTIL_MODULE} PRIVATE
+    $<TARGET_FILE:cfitsio>
+    ZLIB::ZLIB
+    Python3::Module
+)
+target_include_directories(${FITSIDIUTIL_MODULE} PRIVATE
+    ${cfitsio_SOURCE_DIR}
+    ${cfitsio_SOURCE_DIR}/include
+)
+
+install(TARGETS ${FITSIDIUTIL_MODULE}
+    LIBRARY DESTINATION ${SKBUILD_PROJECT_NAME}/fitsidiutil
+    RUNTIME DESTINATION ${SKBUILD_PROJECT_NAME}/fitsidiutil
+)

avica-0.3.1.0/PKG-INFO

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+Metadata-Version: 2.2
+Name: avica
+Version: 0.3.1.0
+Summary: AVICA: Automated VLBI pipeline in CASA
+Author-Email: Avinash Kumar <avialxee@gmail.com>
+License: BSD-3-Clause
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Intended Audience :: Science/Research
+Project-URL: Homepage, https://github.com/avikhagol/avica
+Requires-Python: >=3.9
+Requires-Dist: astropy
+Requires-Dist: numpy
+Requires-Dist: ipython
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: polars
+Requires-Dist: protobuf==3.20.3
+Requires-Dist: typer
+Requires-Dist: importlib_resources>=5.0; python_version < "3.9"
+Provides-Extra: dev
+Requires-Dist: pytest>=3.8; extra == "dev"
+Provides-Extra: all
+Requires-Dist: casatools; extra == "all"
+Requires-Dist: casatasks; extra == "all"
+Requires-Dist: casampi; extra == "all"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Description-Content-Type: text/markdown
+
+VLBI and SMILE-based CASA Optimization (VASCO) pipeline has been renamed to AVICA.
+
+# avica
+AVICA: Automated VLBI pipeline in CASA
+
+
+Documentation : https://avica.readthedocs.io/en/latest/
+
+> submitted to A&A
+
+[![asciicast](https://asciinema.org/a/945113.svg)](https://asciinema.org/a/945113)
+> Demo of the AVICA pipeline running end-to-end.
+
+
+# Installation
+
+> Needs Ubuntu 18.04+, Debian 10+, RHEL/CentOS 8+ \
+> Python >=3.9
+ 
+Since the monolithic version of casa includes its own internal Python 3 installation, 
+it is best to install `avica` within a Python environment that matches the casa version.
+
+<!--Since the monolithic version of casa includes its own internal Python 3 installation, 
+it is best to install avica within a Python environment that matches the casa version.
+
+Specifically, if you are not using the "all" installation option, 
+you should use the casa Python executable itself to create a virtual environment first. For example, for `casa-6.7.0-31-py3.10.el8/` use a virtual environment created using `Python 3.10`. Conda can be used for creating the environment:
+-->
+
+```bash
+   
+   $ path/to/python3 -m venv MY_ENV_DIR
+   $ source MY_ENV_DIR/bin/activate
+
+```
+
+```bash
+
+   $ pip install avica
+
+```
+
+Alternatively, you can use the following installation method, 
+which automatically includes the necessary casa dependency for avica's internal operations.
+
+```bash
+
+   $ pip install avica[all]
+
+```
+
+Note that you must still provide the path to your casadir. 
+This ensures that the pipeline uses the same monolithic casa version, ideally the one downloaded for 
+rPicard to execute specific tasks like mstransform and importfitsidi within an isolated environment.
+
+## Manual
+
+1. Clone the repository to the desired destination.
+
+```
+git clone https://github.com/avikhagol/avica.git
+```
+
+2. Install using `pip`
+
+```bash
+cd avica/
+
+pip install .
+
+```
+
+
+# Usage
+
+
+## Pipeline
+
+```
+Usage: avica pipe run [OPTIONS] [STPS]...                                                                                                                                                                                                                                                                                    
+                                                                                                                                                                                                                                                                                                                              
+ _______________________                                                                                                                                                                                                                                                                                                      
+                                                                                                                                                                                                                                                                                                                              
+ pipeline steps:
+ 
+ -  preprocess_fitsidi
+ -  fits_to_ms
+ -  phaseshift
+ -  avica_avg
+ -  avicameta_ms
+ -  avica_snr
+ -  avica_fill_input
+ -  avica_split_ms
+ -  rpicard
+ 
+ ________________________                                                     
+ 
+      
+╭─ Arguments ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│   stps      [STPS]...  steps for execution [default: preprocess_fitsidi, fits_to_ms, avica_avg, avicameta_ms, avica_snr, avica_fill_input, avica_split_ms, rpicard]                                                                                                                                                        │
+╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --f,--fitsfilenames        TEXT  fitsfile names comma separated                                                                                                                                                                                                                                                            │
+│ --t,--target               TEXT  Selected field / sourc name                                                                                                                                                                                                                                                               │
+│ --configfile               TEXT  config file containing key=value [default: avica.inp]                                                                                                                                                                                                                                     │
+│ --help                           Show this message and exit.                                                                                                                                                                                                                                                               │
+╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+
+
+```
+
+## Manipulating FITS-IDI
+
+To check known FITS-IDI issues run the following:
+
+```
+ Usage: avica fitsidi_check [OPTIONS] [FITSFILENAMES]... COMMAND [ARGS]...                                                                                                                                                                                                                                                         
+                                                                                                                                                                                                                                                                                                                              
+ validate and fix, known FITS-IDI problems                                                                                                                                                                                                                                                                                    
+                                                                                                                                                                                                                                                                                                                              
+╭─ Arguments ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│   fitsfilenames      [FITSFILENAMES]...                                                                                                                                                                                                                                                                                    │
+╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
+│ --fix     --no-fix       [default: no-fix]                                                                                                                                                                                                                                                                                 │
+│ --desc    --no-desc      [default: no-desc]                                                                                                                                                                                                                                                                                │
+│ --help                   Show this message and exit.                                                                                                                                                                                                                                                                       │
+╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+
+
+```
+
+
+#### Example
+
+```
+avica fitsidi_check VLBA_VSN005412_file3.uvfits
++--------------------+---------+-------+-------+----------------+----------+
+| hdu                | fixable | total | fixed | problem_code   | affected |
++==========================================================================+
+| ARRAY_GEOMETRY     | 0       | 8     | 0     | []             | []       |
+| ANTENNA            | 0       | 16    | 0     | []             | []       |
+| FREQUENCY          | 0       | 8     | 0     | []             | []       |
+| PHASE-CAL          | 0       | 12    | 0     | []             | []       |
+| PRIMARY            | 1       | 10    | 0     | ["extra_byte"] | [""]     |
+| SOURCE             | 0       | 8     | 0     | []             | []       |
+| FLAG               | 0       | 12    | 0     | []             | []       |
+| UV_DATA            | 0       | 8     | 0     | []             | []       |
+| GAIN_CURVE         | 0       | 8     | 0     | []             | []       |
+| SYSTEM_TEMPERATURE | 0       | 8     | 0     | []             | []       |
++--------------------+---------+-------+-------+----------------+----------+
+
+```
+
+
+To get the information on the observation run the following:
+
+```
+avica listobs [FITSFILENAMES]... 
+```
+
+
+# Development
+After you clone the repo
+```bash
+
+$ cd avica
+$ pip install -e .[dev]
+```
+
+# Attribution
+
+When using AVICA, please add a link to this repository in a footnote.
+
+# Acknowledgement
+
+"AVICA was developed within the "Search for Milli-Lenses" (SMILE) project. SMILE has received funding from the European Research Council (ERC) under the HORIZON ERC Grants 2021 programme (grant agreement No. 101040021).